From 0168f39eeb1b90c19708b9182b4e14b4421c6df9 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Tue, 13 May 2014 12:54:23 -0400
Subject: [PATCH] r765: fixed a declaration error

Reported by Andreas Tile from Debian
---
 Makefile   | 2 +-
 README.md  | 2 +-
 bwt_lite.c | 2 +-
 main.c     | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/Makefile b/Makefile
index 60c21049..7f9f9755 100644
--- a/Makefile
+++ b/Makefile
@@ -1,6 +1,6 @@
 CC=			gcc
 #CC=			clang --analyze
-CFLAGS=		-g -Wall -Wno-unused-function -O2
+CFLAGS=		-g -Wall -Wextra -Wno-unused-function -O2
 WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS
 AR=			ar
 DFLAGS=		-DHAVE_PTHREAD $(WRAP_MALLOC)
diff --git a/README.md b/README.md
index 548724cf..3e20eacf 100644
--- a/README.md
+++ b/README.md
@@ -93,7 +93,7 @@ settings:
 
 ####Why does a read appear multiple times in the output SAM?
 
-BWA-SW and BWA-MEM perform local alignments.
+BWA-SW and BWA-MEM perform local alignments. 
 
 ####How to map sequences to GRCh38 with ALT contigs?
 
diff --git a/bwt_lite.c b/bwt_lite.c
index 9b472705..0ecb84df 100644
--- a/bwt_lite.c
+++ b/bwt_lite.c
@@ -7,7 +7,7 @@
 #  include "malloc_wrap.h"
 #endif
 
-int is_sa(const uint8_t *T, uint32_t *SA, int n);
+int is_sa(const uint8_t *T, int *SA, int n);
 int is_bwt(uint8_t *T, int n);
 
 bwtl_t *bwtl_seq2bwtl(int len, const uint8_t *seq)
diff --git a/main.c b/main.c
index 51c446c7..9b65696c 100644
--- a/main.c
+++ b/main.c
@@ -4,7 +4,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.8-r764-dirty"
+#define PACKAGE_VERSION "0.7.8-r765-dirty"
 #endif
 
 int bwa_fa2pac(int argc, char *argv[]);